› 6d30

X-ray diffraction
1.17Å resolution

Structure of human Usb1 with uridine-uridine, inactive H208Q mutant

Released:
DOI: 10.2210/pdb6d30/pdb
PDB entry 6d30 coloured by chain, front view.
PDB entry 6d30 coloured by chain, side view.
PDB entry 6d30 coloured by chain, top view.
Source organisms:
Primary publication:
Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.
Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE
Nucleic Acids Res 46 11488-11501 (2018)
PMID: 30215753

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189665 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U6 snRNA phosphodiesterase 1 Chain: A
Molecule details ›
Chain: A
Length: 191 amino acids
Theoretical weight: 22.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BQ65 (Residues: 79-265; Coverage: 71%)
Gene names: C16orf57, Mpn1, USB1
Sequence domains: Uncharacterised conserved protein
Structure domains: Cyclic phosphodiesterase
RNA (5'-R(UP*U)-3') Chain: C
Molecule details ›
Chain: C
Length: 2 nucleotides
Theoretical weight: 567 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 41.698Å b: 53.038Å c: 45.814Å
α: 90° β: 105.72° γ: 90°
R-values:
R R work R free
0.15 0.149 0.172
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer.
Zhou et al. (2023)
7 other articles

3 mentions without citation

The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation.
Huynh et al. (2023)
2 more